Surveillance of zoonoses in livestock and humans: experiences from AHITI interns cohort 5

Surveillance of zoonoses in livestock and humans: experiences from AHITI interns cohort 5

Our participation in the ZooLinK suite of projects will remain memorable. We have acquired sufficient knowledge and experience through the exposure given to us by ZooLinK staff and our participation in the target areas of the project. Since we joined the project on May 2018, we have rotated among the three functional units of the project, namely: (1) veterinary team who visit the livestock markets and slaughterhouses; (2) laboratory team and (3) clinicians team who visit the health centres. The following report will focus on the veterinary team. It describes the activities carried out therein and their relevance to the project.

Two of the interns working in the laboratory (foreground)

A normal ZooLinK day begins with packing the field car with the required consumables a day before the field. Such consumables include; red and purple topped vacutainers, nasal swabs, digital thermometer, heart girth measuring tape, ziplock bags, barcodes, consent forms, faecal pots, gloves, disinfectant, water, coveralls and gumboots etc.

“…our internship has equipped us with adequate disease surveillance skills in the animal field that will help us to extend the knowledge of disease control to farmers…”

In the field, the veterinary team splits into two groups; one group works at the livestock markets and the other at the slaughterhouse. Upon arrival, at the livestock market, the animal is randomly selected and the owner identified to seek consent for sampling the animal and to answer a few questions. If he/she agrees, he/she signs two consent forms one of which goes with the animal owner while the other one remains for ZooLinK records. Before sampling, the animal is humanely restrained to ensure the safety of the animal, handler and person collecting the samples. Physical examination begins before the actual sample collection. Which entails checking for any abnormal discharges from the mouth, eyes, genitals and nose. On the skin swellings and injuries are recorded when present. Nature of the ocular mucous membranes is assessed and recorded, the mouth is checked for any lesions and sores as well the ageing is done from the dentition. The pre-scapula lymph nodes are palpated on both sides to ascertain any enlargement. Lifting of the loose skin of the neck is done to test for skin elasticity. The body condition of the animal is cored in a scale of 1-5. The fleece condition is recorded as either rough or normal and a tape measure used to measure the heart-girth to estimate the weight of the animal. The temperature is taken per-rectal. After the physical examination, the actual collection of the samples begins. Blood is collected from the jugular vein into a red top vacutainer (plain blood) for serology and an EDTA-purple top vacutainer (uncoagulated blood) for parasitology and hematology.

One of the AHITI interns sampling blood from a sheep

Nasal swabs are used to collect swabs from the nose. Nasal swabs are later cultured in the lab and used to test for the presence of Staphylococcus aureus. Fresh faeces are collected per-rectal and placed into a faecal pot. The faecal sample is cultured in the lab to determine the presence of E. coli, Salmonella and Campylobacter. External parasites like ticks, lice etc. are also collected if encountered. The same procedure takes place in the slaughterhouses but in addition, post-motem lesions like cysts, flukes, are recorded and collected inclusive of mesenteric lymph nodes from the pigs.

We are glad to declare that our internship has equipped us with adequate disease surveillance skills in the animal field that will help us to extend the knowledge of disease control to farmers and other stakeholders back at home.

This article was authored by the cohort 5 interns from the Animal Health and Industry Training Institute (AHITI): Sarah Nyambura, John Parkasio and Silas Muriithi.

Farming in transition in East Africa: financial risk taking and agricultural intensification

Farming in transition in East Africa: financial risk taking and agricultural intensification


  • Professor Eric Fèvre, Veterinary Infectious Diseases, Institute of Infection and Global Health
  • Dr Rob Christley, Institute of Infection and Global Health
  • Professor Jude Robinson, Department of Sociology, Social Policy and Criminology

Academic Partner

Dr Salome Buckachi, Institute of Anthropology, Gender and African Studies, University of Nairobi, Kenya

Industry Partner

Financial Sector Development Programme (FSD)-Africa

Funding Details

The PhD Studentship (Tuition fees + stipend of £ 13,726 annually over 4 years) is available for Home/EU students. In addition, a budget for use in own responsibility will be provided.

Project description

Farming in transition in East Africa: financial risk taking and agricultural intensification

In East Africa, and specifically in Kenya (where this study would be based) small-holder livestock production systems, in which farmers grow crops and keep a small diversity of a small number of domestic livestock, are moving from a subsistence model, where farmers grow produce for home consumption, to one of increased commercialisation, intensification and consumer focus (Pretty et al 2011), where the livestock and crops are also grown for commercial gain.  Simultaneously, a greater proportion of Africa’s population is urbanised, making market-oriented farming more important for food security.  This change requires farmers to engage with new value chains for both inputs and outputs.  Shifting from a subsistence system to one in which the market dominates represents a huge financial risk for poor farmers: it requires investment (eg in more farm inputs, in a labour force, in improved breeds of livestock, in transport) and access to more complex financial products (eg loans and credit).  The returns are uncertain, due to market volatility, poorly developed value chains (especially for livestock and animal source foods) and increased exposure to infectious disease problems (improved livestock breeds may be more susceptible to endemic infections).  Despite these risks, such changes are clearly happening throughout Kenya and elsewhere in Africa, because success can reap great financial rewards.

Understanding the motivations behind this risk taking, and the impact it has on the family, how long it takes to generate a return and what sacrifices are made in pursuit of this profit, is a highly relevant objective.  Understanding the changes at an individual farm level would allow extrapolation to understanding these changes on a larger scale, and inform the advice that several intermediaries (NGOs, government, private sector institutions, etc.) give to farmers and policy implementers.  In addition, understanding farmers’ financial decisions can help financial institutions and those who support them to offer tailored, context specific financial products.  Kenya has an impressive history of innovation in the financial services sector, targeting low-income households (eg Mpesa, MShwari, etc).

We are currently implementing a project under the ZELS initiative (Zoonoses in Emerging Livestock Systems), funded by the BBSRC, DFID, ESRC, MRC, NERC and DSTL, which is exploring several aspects of agricultural change in western Kenya.  It provides us with an excellent opportunity to link our existing studies of value chain economics, animal genetics and pathogen surveillance to financial and socio-economic issues of risk-taking in farming.  Our industrial partner, the Financial Sector Development Programme (FSD) – – has previously implemented the Kenya Financial Diary Project ( which tracked the cash flows of 298 low-income Kenyan households over a period of one year.  The diaries, which were designed to capture data across all sectors, and therefore included a relatively small number of livestock farmers in transition, provide an excellent methodology to understand farm-based economics

In this project, the prospective student will select a number (eg up to ~20) of households at different stages of this agricultural transition, and spend a year in the field collecting detailed household financial, economic and social data using the FSD Financial Diary methodology.  Each month, a detailed questionnaire recording relevant financial details and transactions, farm purchases and income will be applied. These data will be supplemented by observations, conversations and some more focussed interviews over the year with different family members (including women) and any casual workers or relatives who are working with the household. Special attention will be paid to changing household dynamics, in particular how traditional and any new tasks are allocated and undertaken within the household, and how any such shifts may challenge traditional gender roles. To supplement the observational data, permission will be sought from participants to photograph and possibly film aspects of the household and landscape that seem pertinent to the study.  Using these data, a comprehensive picture of the social and economic risks taken by farming families, will be gathered.

The project will involve approximately 1 year of in situ fieldwork.  The ideal candidate will be an anthropologist or social scientist with an interest in economics and micro-politics of family life in agricultural communities.  The candidate will be well supported with project related infrastructure at the field site and will have extensive access to the expertise at FSD and its partners.

Secondments: 6 months within FSD’s Africa’s office in Kenya; 3 months at the Institute of Anthropology, Gender and African Studies, University of Nairobi.


Pretty, J., Toulmin, C. and Williams, S. (2011) Sustainable intensification in African agriculture. International Journal of Agricultural Sustainability, 9:1, 5-24.


Important dates

  • Starting Arrangements: October 2016
  • Closing date for applications: 12 February 2016

ZooLinK epidemiology postdoctoral research associate

ZooLinK epidemiology postdoctoral research associate

Institution: Faculty of Health and Life Sciences, Institute of Infection and Global Health, Department of Epidemiology and Population Health

Salary range: £32,277 – £33,242 pa

Location: International Livestock Research Institute campus Nairobi, Kenya

Ref: R-589826/WWW

Closing date for receipt of applications: Wed, 09 Dec 2015 17:00:00 GMT

We are seeking a postdoctoral scientist to contribute to a BBSRC/RCUK/DFID funded research programme entitled “Zoonoses in Livestock in Kenya (ZooLinK)”.  You will be responsible for field management of the project in our study site in Kenya, for managing study design, data and sample collection and for collation and analysis of a large, complex data set focused around the surveillance of zoonotic diseases in domestic livestock and people.  You will be involved in managing a field and laboratory team based in our facility in western Kenya (town of Busia), establishing routine procedures in our diagnostic laboratory, undertaking statistical analysis of data and producing reports and papers for publication in peer reviewed journals.

You will join a large and busy interdisciplinary research team based largely in Kenya, with a base at our partner institute the International Livestock Research Institute (ILRI) in Nairobi and our principal field site in Busia, western Kenya.  You will have visiting scientist status at ILRI.  You will be expected to spend 95% of your time in Kenya, with an initial 80%:20% split between Busia in year 1 and a 60%:40% split in years 2 and 3. You should have a PhD epidemiology, or a closely related subject, with relevant laboratory and field experience, ideally in an African setting. Excellent organisational and communication skills are essential, as is a willingness to travel. The post is available for three years.


Important documents


Applicant information form:

Click to download


Job description file:

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Project Assistant Position – ZooLinK suite of Projects

Project Assistant Position – ZooLinK suite of Projects


A member Center of the CGIAR Consortium

            Position Announcement 

Project Assistant – ZooLinK suite of Projects

REF: PA /AB/06/15

The International Livestock Research Institute (ILRI) seeks to recruit a Project Assistant to support research within the Zoonoses in Livestock in Kenya (ZooLink) Project. He/she will provide project management and coordination support across the ZooLink Project, including co-ordination of personnel, field research logistics, project partner co-ordination, donor interaction, research deliverables, contributions to budget management and other key outputs.  It is 100% funded by a bilateral grant.  ZooLinK is a standalone bilateral project in which ILRI has a major co-ordination role, and this post will be dedicated to delivering that responsibility on behalf of ILRI.

ILRI works with partners worldwide to enhance the roles that livestock play in food security and poverty alleviation, principally in Africa and Asia. The outcomes of these research partnerships help people in developing countries keep their farm animals’ alive and productive, increase and sustain their livestock and farm productivity, find profitable markets for their animal products, and reduce the risk of livestock-related diseases.

A member of the CGIAR Consortium working for a food-secure future, ILRI has its headquarters in Nairobi, Kenya, a principal campus in Addis Ababa, Ethiopia, and offices in other countries in East, West and Southern Africa and in South, Southeast and East Asia.

Apply for this position by clicking here

  1. Program reporting and administration
  • Participate in Project cycle planning, including defining time-lines and deliverable endpoints for all project work packages.
  • Work with academics and students in the project to plan, organize and implement field data collection and laboratory activities.
  • Co-ordinate project components with other members of the ZooLinK project team, on behalf of the PIs.
  • Pro-actively work with all project team members to ensure work plans are documented and on track and to identify problems before they arise, ideally achieved through regular (every 2 weeks) meetings with each of the project teams to oversee ongoing activities and catalyze the solving of any issues.
  • Implement and maintain project database systems for lab and field data collection.
  • Manage existing online collaborative tools and contribute to the creation of new ones.
  • Maintain a contacts database for all project staff, students and visiting academics.
    Maintain the project ZooLinK Document repository.
  • Write monthly summary reports for dissemination to all project members, summarising project progress and progress in meeting project targets.
  • Operate in a split site duty station, being: the field laboratory in Busia, western Kenya and ILRI Headquarters in Nairobi, Kenya.
  • Act as a liaison between the project and other aligned research activities in the institutes (both in Kenya and internationally) involved in the programme.
  • Develop and maintain a Risk register, and assist the PIs in managing risks to the project’s timely delivery.

​2. Budget management

  • Assist the program accountant and budget managers with oversight of the ZooLinK project budget, and liaise with their counterparts at collaborating institutions to ensure timely sharing of budgetary information with senior budget staff.
  • Follow up with the finance department to ensure disbursement of funds to partners.
  • Assist the accounting officer in the monthly routine accounting duties.
  • Oversee day to day ZooLinK project field expenditure.
  • In consultation with the PI and co-PIs, draft ZooLinK annual reports to the donor/funder.
  • Manage stores supply/ordering with external suppliers, and maintain up to date inventories of supplies and consumable shipping, including tracking budgetary allocations for these project activities.
  1. Communication
  • Act as a primary point of contact for all issues related to the ZooLinK project. This will include being the contact person for the project’s primary stakeholders, with whom a long running positive relationship should be established.
  • Assist the project team with coordination of and communication with project partners, including Government officials, collaborators and local administrators
  • Develop and implement a project internal communication strategy, including ensuring that all project meetings are minuted and logged.
  • Participate in the development and implement of a project external communication strategy and assist in compiling regular outputs.
  • Organize conferences, workshops, science write shops, internal and external meetings, project annual retreat and quarterly meetings, and other events as required.
  • Participate actively in annual project meetings, some of which will be held internationally.
  • Contribute to the online presence of the project, including maintaining project website, twitter feed and newsletter.
  • Assist in planning and logistics for project meetings (internal/multi-partner)
  • Bachelor’s Degree in Business Administration, Program Management,  or related field.
  • Master’s Degree in Business Administration, Program Management, or related field will be an added advantage.
  • Professional training in leadership and project management.
  • At least 5 years relevant experience in program management working in an internationally focused research or development organization.
  • Knowledge of administrative and financial management of development programs and/or donor funded projects/programs.
  • Experience in managing work plans, results-based budgets and systems to monitor and report progress.
  • Track record in scientific project management work in either a research or NGO environment.
  • Excellent verbal and written communication skills and an engaging personality.
  • Ability to work in a multi-disciplinary environment.
  • Strong IT skills.
  • Experience with data entry in electronic databases will be an added advantage.
  • Experience of working with epidemiology and public health researchers will be an added advantage.
  • Ability to work in a fast paced environment with interdisciplinary teams of scientists and partner organizations.
  • Ability to communicate with different stakeholders.
  • Understanding of the veterinary public health landscape in Kenya.
  • Ability to handle electronic data entry and data management.
  • Strong English language skills, both written and spoken.
  • Willingness to travel frequently within Kenya, sharing time between Nairobi and Busia, western Kenya.

This is a Nationally Recruited Staff (NRS) position based at ILRI’s Nairobi campus. It is open to Kenyan nationals only. The position is on a 3-year contract, renewable subject to satisfactory performance and availability of funding.

Job level and salary

This position is job level 2C. ILRI offers a competitive salary and benefits package which includes; pension, medical and other insurances for ILRI’s Nationally Recruited Staff.

How to apply: Applicants should send a cover letter and CV explaining their interest in the position, what they can bring to the job and the names and addresses (including telephone and email) of three referees who are knowledgeable about the candidate’s professional qualifications and work experience to the Director, People and Organizational Development through our recruitment portal  before 16 June 2015. The position title and reference number REF: PA /AB/06/15 should be clearly marked on the subject line of the online application.

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ILRI is an equal opportunity employer

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